I use MediaWiki for managing my notes mainly because some of its extensions are very powerful like Sematic MediaWiki and Dynamic Page List. However DevonThink is indispensable in my workflow because it provides the x-devonthink-item URLs which are the building blocks for my hypertexts. If you would like to use them inside a MediaWiki page you should add the following line to the LocalSettings.php file:
$wgUrlProtocols[] = 'x-devonthink-item://';
For more details about this see my blogpost http://organognosi.blogspot.com/2011/02/how-to-use-devonthink-links-in.html